Delete hidden object from commandline pythonscript
You can use the command line to run blender and pass the below python script to it which will delete all unhidden objects:

import bpy
bpy.ops.object.select_all(action='DESELECT')
for obj in bpy.data.objects:
    if obj.hide == True:
        obj.hide = False
        obj.select = True
bpy.ops.object.delete()